I usually just throw my neoprene stuff in the washer on the gentle cycle. Always use powdered detergent and something mild if you have it. Dreft works good, but pricey. I usually just use what I have because I'm cheap. I also put it through the extra rinse. Mine all last years and years. Haven't worn one out yet. Also, a trick for stinky neoprene is to soak it in the washer full of water and a cup of vinegar before you put in the detergent and send it through the cycle. This works great for stinky ol' booties and it doesn't seem to hurt the fabric. Always air dry.
Also, another tip, I would run a load of old towels or something through your washer before you wash anything else after doing your San Juan stuff. That mud sticks around and will stain anything else you put in there. Even better, go to a laundramat!